Is MEF2C p.Lys68fs (c.204_208del) pathogenic?

MEF2C p.Lys68fs (c.204208del) is classified Pathogenic in MEF2C (ClinVar, Single submitter, 1 submitter; last evaluated 2022-11-10). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with MEF2C p.Lys68fs (c.204_208del)?

MEF2C p.Lys68fs (c.204_208del) is associated with Inborn genetic diseases (ClinVar).

How common is MEF2C p.Lys68fs (c.204_208del) in the general population?

MEF2C p.Lys68fs (c.204_208del) is no gnomAD frequency available for this variant (gnomAD).

MEF2C p.Lys68fs

c.204_208del · rs2531279207 · VCV2317249

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 3 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: MEF2C
Protein: p.Lys68fs
Coding: c.204_208del
MANE Select: NM_002397
dbSNP: rs2531279207
Type: Deletion
Location: chr5:88804648 (GRCh38)
Gene constraint: LOEUF 0.212 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 56.80
Residue 68: a DNA-binding region

Full MEF2C gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MEF2C p.Gly202fs Pathogenic ★ same condition
MEF2C p.Thr22fs Pathogenic ★ same condition
MEF2C p.Tyr72fs Pathogenic ★ same condition
MEF2C p.Lys68= Likely benign ★ same residue
MEF2C c.401_402+2del Pathogenic/Likely pathogenic ★★ same condition
MEF2C c.638-2A>C Pathogenic ★★ same condition
MEF2C p.Arg189Ter Pathogenic/Likely pathogenic ★★ same condition
MEF2C p.Leu38Pro Pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/mef2c-p-lys68fs (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown